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comparison psy-maps.xml @ 2:e6d1e9d6b399 draft

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planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
author climate
date Thu, 26 Sep 2024 10:32:08 +0000
parents 706666d912d5
children 988212a7466a
comparison
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1:706666d912d5 2:e6d1e9d6b399
1 <tool id="psy_maps" name="map plot" version="1.2.1"> 1 <tool id="psy_maps" name="map plot" version="1.3.0" profile="23.0">
2 <description>gridded (lat/lon) netCDF data</description> 2 <description>gridded (lat/lon) netCDF data</description>
3 <edam_topics>
4 <edam_topic>topic_3855</edam_topic>
5 <edam_topic>topic_3318</edam_topic>
6 </edam_topics>
7 <edam_operations>
8 <edam_operation>operation_0573</edam_operation>
9 </edam_operations>
3 <requirements> 10 <requirements>
4 <requirement type="package" version="3">python</requirement> 11 <requirement type="package" version="3">python</requirement>
5 <requirement type="package" version="1.2.1">psyplot</requirement> 12 <requirement type="package" version="1.4.3">psyplot</requirement>
6 <requirement type="package" version="1.2.0">psy-maps</requirement> 13 <requirement type="package" version="1.4.2">psy-maps</requirement>
7 <requirement type="package" version="1.2.0">psy-reg</requirement> 14 <requirement type="package" version="1.4.0">psy-reg</requirement>
8 <requirement type="package" version="1.4.2">netcdf4</requirement> 15 <requirement type="package" version="1.6.5">netcdf4</requirement>
9 </requirements> 16 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
11 HOME=`pwd` &&
12 python3 '$__tool_directory__/psymap_simple.py' 18 python3 '$__tool_directory__/psymap_simple.py'
13 '$ifilename' '$variable' 19 '$ifilename' '$variable'
20 --logscale '$adv.logscale'
14 --proj '$adv.projection' 21 --proj '$adv.projection'
15 --cmap '$adv.colormap' 22 --cmap '$adv.colormap'
16 --output image.png 23 --output image.png
17 #if str($adv.multiple_plot.selector) == 'yes' 24 #if str($adv.multiple_plot.selector) == 'yes'
18 --time '$adv.multiple_plot.time' 25 --time '$adv.multiple_plot.time'
42 </when> 49 </when>
43 <when value="no"> 50 <when value="no">
44 <param name="title" type="text" value="" label="plot title" /> 51 <param name="title" type="text" value="" label="plot title" />
45 </when> 52 </when>
46 </conditional> 53 </conditional>
54 <param name="logscale" type="select" label="log scale the data">
55 <option value="yes">yes</option>
56 <option value="no" selected="true">no</option>
57 </param>
47 <param name="projection" type="select"> 58 <param name="projection" type="select">
48 <option value="" selected="true">PlateCarree</option> 59 <option value="" selected="true">PlateCarree</option>
49 <option value="robin">Robinson</option> 60 <option value="robin">Robinson</option>
50 <option value="moll">Mollweide</option> 61 <option value="moll">Mollweide</option>
51 <option value="geo">Geostationary</option> 62 <option value="geo">Geostationary</option>
153 <param name="variable" value="TS" /> 164 <param name="variable" value="TS" />
154 <param name="projection" value="ortho" /> 165 <param name="projection" value="ortho" />
155 <param name="colormap" value="RdBu_r" /> 166 <param name="colormap" value="RdBu_r" />
156 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12_ortho.png" compare="sim_size" delta="500"/> 167 <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12_ortho.png" compare="sim_size" delta="500"/>
157 </test> 168 </test>
169 <test>
170 <param name="ifilename" value="ESACCI-OC-L3S-CHLOR_A-20220601-RESIZED-fv6.0.nc" />
171 <param name="variable" value="chlor_a" />
172 <param name="projection" value="" />
173 <param name="colormap" value="jet" />
174 <param name="logscale" value="yes" />
175 <output name="ofilename" ftype="png" file="ESACCI-OC-L3S-CHLOR_A-20220601-RESIZED-fv6.0.png" compare="sim_size" delta="1500"/>
176 </test>
158 </tests> 177 </tests>
159 <help><![CDATA[ 178 <help><![CDATA[
160 179
161 **Visualization on a map with psyplot** 180 **Visualization on a map with psyplot**
162 ========================================= 181 =========================================
165 184
166 185
167 .. class:: infomark 186 .. class:: infomark
168 187
169 The wrappers aims at providing the same functionality as ``psyplot.plot.mapplot`` but it has some limitations. 188 The wrappers aims at providing the same functionality as ``psyplot.plot.mapplot`` but it has some limitations.
170 The input file must be in netCDF format and must contain 2D arrays with geographical coordinatates 189 The input file must be in netCDF format and must contain 2D arrays with geographical coordinatates
171 (latitudes, longitudes) given in degrees. 190 (latitudes, longitudes) given in degrees.
172 TODO: Fill in help. 191 The code may fail when the data is significantly different from what has been tested.
173 192
174 **What it does** 193 **What it does**
175 ---------------- 194 ----------------
176 195
177 This tools creates an image (png format) corresponding to the visualization on a geographical map of a variable extracted from a 196 This tools creates an image (png format) corresponding to the visualization on a geographical map of a variable extracted from a
178 netCDF file (input file). By default, the projection is ``PlateCarree`` and colormap is ``jet``. These settings can be changed in *Advanced settings*. 197 netCDF file (input file).
198 By default, the projection is ``PlateCarree`` and colormap is ``jet``.
199 These settings can be changed in *Advanced settings* alongside an option to log scale the plot.
179 200
180 201
181 **Usage** 202 **Usage**
182 203
183 :: 204 ::
184 205
185 usage: psymap_simple.py [-h] [--proj PROJ] [--cmap CMAP] [--output OUTPUT] [--time TIME] 206 usage: psymap_simple.py [-h] [--proj PROJ] [--cmap CMAP] [--output OUTPUT] [--time TIME]
186 [--format FORMAT] [--title TITLE] [--ncol NCOL] [--nrow NROW] [-v] input varname 207 [--format FORMAT] [--title TITLE] [--ncol NCOL] [--nrow NROW] [-l] [-v] input varname
187 208
188 209
189 Positional arguments: 210 Positional arguments:
190 ~~~~~~~~~~~~~~~~~~~~~ 211 ~~~~~~~~~~~~~~~~~~~~~
191 212
192 - **input**: input filename with geographical coordinates (netCDF format) 213 - **input**: input filename with geographical coordinates (netCDF format)
193 - **varname**: Specify which variable to plot (case sensitive) 214 - **varname**: specify which variable to plot (case sensitive)
194 215
195 Optional arguments: 216 Optional arguments:
196 ~~~~~~~~~~~~~~~~~~~~~ 217 ~~~~~~~~~~~~~~~~~~~~~
197 218
198 -h, --help show this help message and exit 219 -h, --help show this help message and exit
199 --proj PROJ Specify the projection on which we draw 220 -l, --logscale log scale the data
200 --cmap CMAP Specify which colormap to use for plotting 221 --proj PROJ specify the projection on which we draw
222 --cmap CMAP specify which colormap to use for plotting
201 --output OUTPUT output filename to store resulting image (png format) 223 --output OUTPUT output filename to store resulting image (png format)
202 -v, --verbose switch on verbose mode 224 -v, --verbose switch on verbose mode
203 --time TIME list of times to plot for multiple plots 225 --time TIME list of times to plot for multiple plots
204 --format FORMAT format for date/time (default is Month d, yyyy) 226 --format FORMAT format for date/time (default is Month d, yyyy)
205 --title TITLE plot title 227 --title TITLE plot title
209 It uses psy-maps, a python package to generate plots. More information about 231 It uses psy-maps, a python package to generate plots. More information about
210 psyplot and psy-maps can be found at https://psyplot.readthedocs.io/projects/psy-maps/en/latest/ 232 psyplot and psy-maps can be found at https://psyplot.readthedocs.io/projects/psy-maps/en/latest/
211 233
212 ]]></help> 234 ]]></help>
213 <citations> 235 <citations>
236 <citation type="doi">10.21105/joss.00363</citation>
214 </citations> 237 </citations>
215 </tool> 238 </tool>